I wound up getting a ride from Sonoma to Petaluma and then catching the Golden Gate Transit bus back to my hostel.
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Christine LettsAug 27 '11 at 6:46

Transit tangent: depending on what you want to do in San Francisco, BART may not be the best transit option. MUNI blankets most of the city with routes and stops; BART is just one line through it.
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bneelyFeb 4 '12 at 12:53

On that map, draw a vertical line down between Sonoma and St. Helena, and a horizontal line between Novato and Petaluma. The area from the top left corner down to where your two lines meet is Sonoma County.

Looking at the maps and schedules, the direct bus routes are Route 80 and Route 101, both of which leave San Francisco from:

San Francisco (Folsom & 7th)

Main & Folsom (Temporary Transbay Terminal)

San Francisco (Mission & 1st)

SF Civic Center (McAllister & Polk)

The next thing you'll have to figure out is where you want to go: the city of Sonoma, Sonoma Valley, or Sonoma County? For the first two, you'll have to get off (probably in Petaluma) and transfer to a local bus.

Depending on what it is you want to do in Wine Country, I'd recommend staying on all the way through Santa Rosa—just north of there is where things really get beautiful, in my thoroughly biased opinion.